<!--
Created: 12 Dec 2009
-->
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta NAME="description" CONTENT="Image import using OSRA">
<meta NAME="keywords" CONTENT="OSRA, image, import, Marvin">
<meta NAME="author" CONTENT="Peter Vadasz">   
<link REL ="stylesheet" TYPE="text/css" HREF="../marvinmanuals.css" TITLE="Style">
<title>Image import in Marvin</title>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<h1>Image import in Marvin</h1>

<h2>Contents</h2>
<ul>
<li><a href="#osra">OSRA software and integration into Marvin</a></li>
<li><a href="#usage">Using OSRA in Marvin</a></li>
<li><a href="#problems">Common problems</a></li>
</ul>

<h2><a class="anchor" name="osra">OSRA software and integration into Marvin</a></h2>
<p>
OSRA is a utility designed to convert graphical representations of chemical structures.
</p>
<p>
Since Marvin version 5.3.0 images can be imported from files, and pasted into Marvin
using the OSRA sofware.
</p>

<p>
</p>

<h2><a class="anchor" NAME="usage">Using OSRA in Marvin</a></h2>
<p>
To make OSRA usable in Marvin:
<ul>
 <li> Install the OSRA software (installers are available for Windows and Mac,
      and it can be installed from source for Linux, Unix).</li>
 <li> Set the OSRA environment variable as the absolute path of the directory,
      where OSRA is installed.</li>
</ul>
</p>

<p>
Two methods are available to import images into MarvinSketch:
<ul>
 <li> Opening an image chosen by a file chooser (File menu/Open image... item
      by default).</li>
 <li> If there is an image on the clipboard, the default Marvin paste will
      paste the image using OSRA.</li>
</ul>
</p>

<h2><a class="anchor" name="problems">Common problems</a></h2>

<p>
Common problems quoted from OSRA home page:
</p>
<p>
"Note that any software designed for optical recognition is unlikely to be perfect,
and the output produced might, and probably will, contain errors, so a curation by a
human knowledgeable in chemical structures is highly recommended." 
</p>
<p>
So OSRA sometimes can not recognize a chemical structure or do some mistakes,
and there are issues easy to forget about OSRA. These are the most common of problems: 
<ul>
<li> OSRA can not open small images, and molecules. If a molecule contains 
    less than 6 molecules, or smaller than 20*20 pixels (depending also from
    resolution, and font size) OSRA will most likely fail to recognize the structure.</li>
<li> OSRA may need programs installed on the computer to process with special 
    types. To open a pdf/ps file Adobe Acrobat Reader/Ghostscript has to be
    installed on the computer.</li>
<li> OSRA can not open all image file types perfectly. Converting the image
    in different formats and importing them shows that there are formats OSRA
    easier recognize. So in some cases conversion to png file format helps
    (png seems to be the most OSRA friendly format).</li>
<li> OSRA has to be installed on your computer and the OSRA environment
    variable be set as the absolute path of the install directory. (If the
    import menu item is not enabled surely this is the problem. After installing
    OSRA and/or setting the variable Marvin must be restarted to make image import available.)</li>
</ul>
</p>

<p ALIGN=LEFT>
<small>Marvin uses <a HREF="http://osra.sourceforge.net">OSRA</a> software
    for image import by <a HREF=""http://cactus.nci.nih.gov/osra>CADD Group Chemoinformatics Tools and User Services</a>

</small>
</p>

</body>
</html>
